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35 # Python setuptools script to build and install the gmxapi Python interface
36 # from a GROMACS installation directory.
38 # Usage note: things go smoothly when we stick to the setup.py convention of
39 # having a package source directory with the same name as the package at the
40 # same level as the setup.py script and only expect `pip install .` in the
41 # setup.py directory. If we play with the layout more, it is hard to keep all
42 # of the `pip` and `setup.py` cases working as expected. This is annoying
43 # because running the Python interpreter immediately from the same directory
44 # can find the uninstalled source instead of the installed package. We can
45 # ease this pain by building an sdist in the enclosing CMake build scope
46 # and encouraging users to `pip install the_sdist.archive`. Otherwise, we
47 # just have to document that we only support full build-install of the Python
48 # package from the directory containing setup.py, which may clutter that
49 # directory with some artifacts.
53 # Import setuptools early to avoid UserWarning from Distutils.
54 # Ref: https://gitlab.com/gromacs/gromacs/-/issues/3715
57 # Allow setup.py to be run when scikit-build is not installed, such as to
58 # produce source distribution archives with `python setup.py sdist`
60 from skbuild import setup
62 from distutils.core import setup
65 The `gmxapi` package requires an existing GROMACS installation, version 2020 or higher.
66 To specify the GROMACS installation to use, provide a GMXTOOLCHAINDIR
67 environment variable when running setup.py or `pip`.
70 GMXTOOLCHAINDIR=/path/to/gromacs/share/cmake/gromacs pip install gmxapi
72 If you have multiple builds of GROMACS, distinguished by a suffix `$SUFFIX`, the
73 tool chain directory will use that suffix.
76 GMXTOOLCHAINDIR=/path/to/gromacs/share/cmake/gromacs$SUFFIX pip install gmxapi
78 In the example, `gmxapi` is downloaded automatically from pypi.org. You can
79 replace `gmxapi` with a local directory or archive file to build from a source
82 setup.py will use the location of GMXTOOLCHAINDIR to locate the
83 gmxapi library configured during GROMACS installation. Alternatively, if
84 gmxapi_DIR is provided, or if GMXRC has been "sourced", the toolchain file
85 location may be deduced. Note, though, that if multiple GROMACS installations
86 exist in the same location (with different suffixes) only the first one will be
87 used when guessing a toolchain, because setup.py does not know which corresponds
88 to the gmxapi support library.
90 If specifying GMXTOOLCHAINDIR and gmxapi_DIR, the tool chain directory must be
91 located within a subdirectory of gmxapi_DIR.
93 Refer to project web site for complete documentation.
98 class GmxapiInstallError(Exception):
99 """Error processing setup.py for gmxapi Python package."""
102 gmx_toolchain_dir = os.getenv('GMXTOOLCHAINDIR')
103 gmxapi_DIR = os.getenv('gmxapi_DIR')
104 if gmxapi_DIR is None:
105 # Infer from GMXRC exports, if available.
106 gmxapi_DIR = os.getenv('GROMACS_DIR')
109 def _find_first_gromacs_suffix(directory):
110 dir_contents = os.listdir(directory)
111 for entry in dir_contents:
112 if entry.startswith('gromacs'):
113 return entry.strip('gromacs')
116 if gmx_toolchain_dir is None:
117 # Try to guess from standard GMXRC environment variables.
118 if gmxapi_DIR is not None:
119 if os.path.exists(gmxapi_DIR) and os.path.isdir(gmxapi_DIR):
120 share_cmake = os.path.join(gmxapi_DIR, 'share', 'cmake')
121 suffix = _find_first_gromacs_suffix(share_cmake)
122 if suffix is not None:
123 gmx_toolchain_dir = os.path.join(share_cmake, 'gromacs' + suffix)
125 if gmx_toolchain_dir is None:
127 raise GmxapiInstallError('Could not configure for GROMACS installation. Provide GMXTOOLCHAINDIR.')
129 suffix = os.path.basename(gmx_toolchain_dir).strip('gromacs')
130 gmx_toolchain = os.path.abspath(os.path.join(gmx_toolchain_dir, 'gromacs-toolchain' + suffix + '.cmake'))
132 if gmxapi_DIR is None:
133 # Example: given /usr/local/gromacs/share/cmake/gromacs/gromacs-toolchain.cmake,
134 # we would want /usr/local/gromacs.
135 # Note that we could point more directly to the gmxapi-config.cmake but,
136 # so far, we have relied on CMake automatically looking into
137 # <package>_DIR/share/cmake/<package>/ for such a file.
138 # We would need a slightly different behavior for packages that link against
139 # libgromacs directly, as sample_restraint currently does.
140 gmxapi_DIR = os.path.join(os.path.dirname(gmx_toolchain), '..', '..', '..')
142 gmxapi_DIR = os.path.abspath(gmxapi_DIR)
144 if not os.path.exists(gmxapi_DIR) or not os.path.isdir(gmxapi_DIR):
146 raise GmxapiInstallError('Please set a valid gmxapi_DIR.')
148 if gmxapi_DIR != os.path.commonpath([gmxapi_DIR, gmx_toolchain]):
149 raise GmxapiInstallError('GROMACS toolchain file {} is not in gmxapi_DIR {}'.format(
154 cmake_platform_hints = '-DCMAKE_TOOLCHAIN_FILE={}'.format(gmx_toolchain)
155 # Note that <package>_ROOT is not standard until CMake 3.12
156 # Reference https://cmake.org/cmake/help/latest/policy/CMP0074.html#policy:CMP0074
157 cmake_gmxapi_hint = '-Dgmxapi_ROOT={}'.format(gmxapi_DIR)
158 cmake_args = [cmake_platform_hints, cmake_gmxapi_hint]
163 # TODO: single-source version information (currently repeated in gmxapi/version.py and CMakeLists.txt)
165 python_requires='>=3.6',
166 install_requires=['networkx>=2.0',
169 packages=['gmxapi', 'gmxapi.simulation'],
170 package_data={'gmxapi': ['gmxconfig.json']},
172 cmake_args=cmake_args,
174 author='M. Eric Irrgang',
175 author_email='info@gmxapi.org',
176 description='gmxapi Python interface for GROMACS',
178 url='http://gmxapi.org/',
180 # The installed package will contain compiled C++ extensions that cannot be loaded
181 # directly from a zip file.